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- PDB-2ot4: Structure of a hexameric multiheme c nitrite reductase from the e... -

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Basic information

Entry
Database: PDB / ID: 2ot4
TitleStructure of a hexameric multiheme c nitrite reductase from the extremophile bacterium Thiolkalivibrio nitratireducens
ComponentsEight-heme nitrite reductase
KeywordsOXIDOREDUCTASE / cytochrome c nitrite reductase / NrfA / sulfite reductase
Function / homology
Function and homology information


ammonium ion metabolic process / nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / anaerobic electron transport chain / nitrate assimilation / outer membrane-bounded periplasmic space / calcium ion binding / heme binding
Similarity search - Function
Helix Hairpins - #3080 / Cytochrome c552 / Cytochrome c552 / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Multiheme cytochrome c family profile. / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Multiheme cytochrome superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Helix Hairpins ...Helix Hairpins - #3080 / Cytochrome c552 / Cytochrome c552 / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Multiheme cytochrome c family profile. / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Multiheme cytochrome superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / HEME C / Cytochrome c-552 / Cytochrome c-552
Similarity search - Component
Biological speciesThioalkalivibrio nitratireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsPolyakov, K.M. / Boyko, K.M. / Slutsky, A. / Tikhonova, T.V. / Antipov, A.N. / Zvyagilskaya, R.A. / Popov, A.N. / Lamzin, V.S. / Bourenkov, G.P. / Popov, V.O.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: High-resolution structural analysis of a novel octaheme cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens.
Authors: Polyakov, K.M. / Boyko, K.M. / Tikhonova, T.V. / Slutsky, A. / Antipov, A.N. / Zvyagilskaya, R.A. / Popov, A.N. / Bourenkov, G.P. / Lamzin, V.S. / Popov, V.O.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and preliminary X-ray analysis of cytochrome c nitrite reductase from Thialkalivibrio nitraterecense.
Authors: Boyko, K.M. / Polyakov, K.M. / Tikhonova, T.V. / Slutsky, A. / Antipov, A.N. / Zvyagilskaya, R.A. / Bourenkov, G.P. / Popov, A.N. / Lamzin, V.S. / Popov, V.O.
#2: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 2006
Title: Molecular and catalytic properties of a novel cytochrome c nitrite reductase from nitrate-reducing haloalkaliphic sulfur-oxidixing bacterium Thioalkalivibrio nitratireducens.
Authors: Tikhonova, T.V. / Slutsky, A. / Antipov, A.N. / Boyko, K.M. / Polyakov, K.M. / Sorokin, D.Y. / Zvyagilskaya, R.A. / Popov, V.O.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structures of complexes of octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens with sulfite and cyanide.
Authors: Trofimov, A.A. / Polyakov, K.M. / Boyko, K.M. / Tikhonova, T.V. / Safonova, T.N. / Tikhonov, A.V. / Popov, A.N. / Popov, V.O.
#4: Journal: Crystallography Reports / Year: 2010
Title: Structure of octaheme cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens in a complex with phosphate
Authors: Trofimov, A.A. / Polyakov, K.M. / Boiko, K.M. / Filimonenkov, A.A. / Dorovatovskii, P.V. / Tikhonova, T.V. / Popov, V.O. / Kovalchuk, M.V.
History
DepositionFeb 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Remark 400COMPOUND UNUSUAL COVALENT BOND WAS DETECTED IN THE ACTIVE SITE OF THE ENZYME BETWEEN S ATOM OF ...COMPOUND UNUSUAL COVALENT BOND WAS DETECTED IN THE ACTIVE SITE OF THE ENZYME BETWEEN S ATOM OF CYS305 AND ORTHO-POSITION OF TYR303.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eight-heme nitrite reductase
B: Eight-heme nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,98028
Polymers118,9852
Non-polymers10,99626
Water21,9241217
1
A: Eight-heme nitrite reductase
B: Eight-heme nitrite reductase
hetero molecules

A: Eight-heme nitrite reductase
B: Eight-heme nitrite reductase
hetero molecules

A: Eight-heme nitrite reductase
B: Eight-heme nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)389,94084
Polymers356,9546
Non-polymers32,98778
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area94420 Å2
ΔGint-1294.8 kcal/mol
Surface area95860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.917, 193.917, 193.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-3319-

HOH

21B-2919-

HOH

DetailsThe biological assembly is a hexamer generated from the dimer in the asymmetric unit(chain A and chain B) by the following operations: z-1/2, -x+1/2, -y+1 and -y+1/2, -z+1, x+1/2.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Eight-heme nitrite reductase


Mass: 59492.293 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thioalkalivibrio nitratireducens (bacteria)
Strain: ALEN 2 / References: UniProt: Q5F2I3, UniProt: L0DSL2*PLUS

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Non-polymers , 6 types, 1243 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1217 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: The drop contained 5mkl of enzyme solution (14.5 mg/ml) in 0.005 M Tris-borat buffer (pH 8.7) and 5 mkl reservoir solution. The reservoir solution contained 26.3% MPD, 0.175 M ammonium ...Details: The drop contained 5mkl of enzyme solution (14.5 mg/ml) in 0.005 M Tris-borat buffer (pH 8.7) and 5 mkl reservoir solution. The reservoir solution contained 26.3% MPD, 0.175 M ammonium acetate in 0.09 M sodium citrate buffer (pH 5.6), VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.96, 1.7375
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.961
21.73751
ReflectionResolution: 1.5→30 Å / Num. obs: 373791 / % possible obs: 97.4 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.036 / Χ2: 1.241 / Net I/σ(I): 17.1
Reflection shellResolution: 1.5→1.52 Å / Rmerge(I) obs: 0.476 / Num. unique all: 12460 / Χ2: 1.764 / % possible all: 98.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→24.04 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.22 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.141 11295 3 %RANDOM
Rwork0.126 ---
obs0.127 373155 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.294 Å2
Refine analyzeLuzzati coordinate error obs: 0.137 Å
Refinement stepCycle: LAST / Resolution: 1.5→24.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8228 0 759 1217 10204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0219691
X-RAY DIFFRACTIONr_bond_other_d0.0020.025975
X-RAY DIFFRACTIONr_angle_refined_deg1.5752.1713309
X-RAY DIFFRACTIONr_angle_other_deg1.0933.00514380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14351057
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13823.817469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.279151401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9811566
X-RAY DIFFRACTIONr_chiral_restr0.0960.21236
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0210907
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021927
X-RAY DIFFRACTIONr_nbd_refined0.2220.22052
X-RAY DIFFRACTIONr_nbd_other0.2040.27235
X-RAY DIFFRACTIONr_nbtor_refined0.1920.24578
X-RAY DIFFRACTIONr_nbtor_other0.090.24480
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2895
X-RAY DIFFRACTIONr_metal_ion_refined0.0320.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3030.2176
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.253
X-RAY DIFFRACTIONr_mcbond_it1.3771.55366
X-RAY DIFFRACTIONr_mcbond_other0.6921.52116
X-RAY DIFFRACTIONr_mcangle_it1.90328479
X-RAY DIFFRACTIONr_scbond_it2.68535107
X-RAY DIFFRACTIONr_scangle_it3.5614.54793
X-RAY DIFFRACTIONr_rigid_bond_restr1.423317851
X-RAY DIFFRACTIONr_sphericity_free7.89731217
X-RAY DIFFRACTIONr_sphericity_bonded3.902315241
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 804 -
Rwork0.171 26773 -
obs-27577 100 %

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